Пример #1
0
def run(argv):
    opts = util.parse_docopt(__doc__, argv, False)
    image       = opts['<image>']
    fastq_file  = opts['--input']
    contig_file = opts['--output']
    task        = opts['--task']

    if not ctn.image_available(image):
        util.err_exit('unknown_image', {'image': image})

    cntr_src_dir = "/fastq"
    biobox_yaml = fle.generate([
        fle.fastq_arguments(cntr_src_dir, [fastq_file, "paired"])])

    host_src_dir = os.path.abspath(os.path.dirname(fastq_file))
    host_dst_dir = tmp.mkdtemp()

    mount_strings = [
        ctn.mount_string(host_src_dir, cntr_src_dir),
        ctn.biobox_file_mount_string(fle.create_biobox_directory(biobox_yaml)),
        ctn.output_directory_mount_string(host_dst_dir)]

    ctn.run(ctn.create(image, task, mount_strings))
    biobox_output = fle.parse(host_dst_dir)
    copy_contigs_file(host_dst_dir, biobox_output, contig_file)
Пример #2
0
def run(argv):
    opts = util.parse_docopt(__doc__, argv, False)
    image = opts['<image>']
    fastq_file = opts['--input']
    contig_file = opts['--output']
    task = opts['--task']

    if not ctn.image_available(image):
        util.err_exit('unknown_image', {'image': image})

    cntr_src_dir = "/fastq"
    biobox_yaml = fle.generate(
        [fle.fastq_arguments(cntr_src_dir, [fastq_file, "paired"])])

    host_src_dir = os.path.abspath(os.path.dirname(fastq_file))
    host_dst_dir = tmp.mkdtemp()

    mount_strings = [
        ctn.mount_string(host_src_dir, cntr_src_dir),
        ctn.biobox_file_mount_string(fle.create_biobox_directory(biobox_yaml)),
        ctn.output_directory_mount_string(host_dst_dir)
    ]

    ctn.run(ctn.create(image, task, mount_strings))
    biobox_output = fle.parse(host_dst_dir)
    copy_contigs_file(host_dst_dir, biobox_output, contig_file)
Пример #3
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def test_checking_an_available_image_with_tag():
    nose.assert_equal(ctn.image_available("python:2.7"), True)
Пример #4
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def test_checking_an_available_image():
    nose.assert_equal(ctn.image_available("python"), True)
Пример #5
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def test_checking_an_available_image_with_tag():
    nose.assert_equal(ctn.image_available("python:2.7"), True)
Пример #6
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def test_checking_an_available_image():
    nose.assert_equal(ctn.image_available("python"), True)